Table 1.

Lead SNPs in discovery and replication

						Discovery						Replication
CHR	BP	Locus	SNP	Type of variation	EA/NEAa	EAFb	ORc	Pd	Directione	I2 f	Phet g	EAF	OR	Ph	Direction	I2	Phet
1	205484373	CDK18	rs138760780	Intronic	T/C	0.018	3.48	9.20 10−6	+++	0	0.943	0.020	1.88	0.014	++++−	0	0.509
2	97455276	CNNM4	rs116656846	Intronic	A/G	0.023	2.57	9.88 10−6	+++	0	0.661	0.028	0.89	0.696	−+−	0	0.876
2	155225182	GALNT13	rs17206992	Intronic	G/A	0.057	2.32	6.33 10−6	+++	0	0.817	0.052	0.97	0.580	++−+−	0	0.934
2	177645590	AC092162.1	rs113517532	Intergenic	AGAT/A	0.106	1.75	1.90 10−6	+++	0	0.912	0.105	0.86	0.887	+−+−	0	0.658
3	13370674	NUP210	rs73018809	Intronic	T/A	0.024	3.50	1.89 10−7	+++	59.1%	0.087	0.022	0.60	0.955	−+	0	0.722
3	103975418	MIR548A3	rs28641753	Intergenic	T/C	0.071	2.10	1.59 10−7	+++	0	0.863	0.067	1.02	0.440	−++−	62.70%	0.030
4	6171230	JAKMIP1	rs78031527	Intronic	T/C	0.201	1.70	5.41 10−6	+++	0	0.493	0.209	1.13	0.114	++−+−	0	0.622
5	10500646	ROPN1L	rs143537377	Intronic	C/A	0.096	1.88	7.89 10−6	+++	1.1%	0.577	0.100	0.85	0.885	−+−+	19.20%	0.292
5	71394387	MAP1B	rs115829748	Intergenic	T/C	0.040	3.16	1.36 10−9	+++	71.9%	0.028	0.036	1.13	0.283	−+++−	0	0.655
6	95557471	MANEA-AS1	rs9354144	Intergenic	A/T	0.105	1.71	5.78 10−6	+++	0	0.785	0.097	1.05	0.330	−++−	23.90%	0.262
8	73842523	KCNB2	rs571622299	Intronic	A/G	0.015	4.12	6.47 10−6	+++	47.2%	0.150	NA	NA	NA	NA	NA	NA
9	37034095	PAX5	rs143723948	UTR5	T/C	0.499	1.65	6.01 10−7	+++	0	0.985	NA	NA	NA	NA	NA	NA
9	71955717	FAM189A2	rs12344245	Intronic	G/A	0.035	2.52	9.23 10−6	+++	0	0.950	0.038	1.45	0.022	+−+++	0	0.560
10	19457387	ARL5B	rs117826205	Intronic	C/T	0.026	2.72	6.30 10−6	+++	0	0.482	0.029	1.11	0.315	−++	5.70%	0.374
11	8080425	TUB	rs61879614	Intronic	C/T	0.048	2.94	2.60 10−6	+++	9.4%	0.332	0.046	1.11	0.300	+−	0	0.775
16	2160973	PKD1	rs116092985	Missense (W1399R)	G/A	0.097	1.85	1.72 10−5	+++	29.5%	0.242	0.096	1.29	0.026	++++−	0	0.488
17	4328164	SPNS3	rs34319244	Intergenic	C/CT	0.440	1.51	2.59 10−6	+++	48.8%	0.142	NA	NA	NA	NA	NA	NA
18	45399356	SMAD2	rs113114656	Intronic	T/C	0.040	2.67	2.30 10−6	+++	2.4%	0.359	0.038	1.04	0.437	−++−+	43.40%	0.132
21	21347156	NCRNA00320	rs67213764	Intergenic	G/A	0.261	1.48	9.28 10−6	+++	0	0.536	0.260	1.03	0.363	++−	32.20%	0.207
21	24929109	AP000459.7	rs12482425	Intergenic	A/G	0.314	0.66	9.33 10−6	−	0	0.509	0.308	1.09	0.871	+++++	0	0.931
22	25988780	ADRBK2	rs373009901	Intronic	C/G	0.019	3.94	9.42 10−6	+++	0	0.599	NA	NA	NA	NA	NA	NA

^aEstimated allele/non estimated allele

^bAllele frequency of the estimate allele

^cOdds ratio for disease

^dAssociation p value derived from the meta-analysis of the three discovery cohorts

^eDirectionality of the effects across the contributing cohorts

^fI² statistics for heterogeneity across the contributing cohorts

^gp value for homogeneity across the contributing cohorts

^hOne sided test p value of association